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cite="mid:ea92b94b-4d36-76c7-86e6-7ab94351b44c@creatis.insa-lyon.fr">
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<p>Ruoyan,</p>
<p><br>
</p>
<p>From the shroud image, the signal extraction sometimes fails to
find the period of the motion of the diaphragm, which results in
incorrect phase detection. The easiest way to make sure your
respiratory phase has been correctly detected is to used the
following python script:</p>
<p><a class="moz-txt-link-freetext"
href="https://www.creatis.insa-lyon.fr/%7Emory/showPeaksOverShroud.py"
moz-do-not-send="true">https://www.creatis.insa-lyon.fr/~mory/showPeaksOverShroud.py</a></p>
<p><br>
</p>
<p>You have to save your shroud image with .mhd extension, because
simpleRTK can't read .mha (I think), so modify the command line
that generates it (in the 4DROOSTER wiki page, that would be <br>
</p>
<pre class="de1">rtkamsterdamshroud <span class="re5">--path</span> . \
<span class="re5">--regexp</span> <span class="st_h">'.*.his'</span> \
<span class="re5">--output</span> shroud.mha \
<span class="re5">--unsharp</span> <span class="nu0">650)
</span></pre>
<span class="nu0">Change "shroud.mha" into "shroud.mhd", re-run
all command lines except the ROOSTER reconstruction, and then
run <br>
<br>
</span>"showPeaksOverShroud.py <span class="nu0">shroud.mhd
sphase.txt"</span><br>
<span class="nu0"></span><span class="nu0"></span><br>
It will generate an RGB image named "peaksOverShroud.png", which
shows the shroud, and overlays the detected extrema of the phase.
If your detection is wrong, you'll see it. The script requires
SimpleRTK, python and a few python libs. <br>
<br>
If your peaks detection is indeed incorrect, you can try cropping
the shroud to the region where the periodic signal is most
visible. This is usually sufficient. If you need more help, send
over your shroud.mhd and shroud.raw file.<br>
<br>
Regards,<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 09/01/2018 15:47, ry.meng wrote:<br>
</div>
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cite="mid:5D207BEE-6153-4D53-BD0C-6CD67BE69149@siat.ac.cn">
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<div style="line-height: 22.4px;">Hi <span
style="line-height: 22.4px;">Cyril, </span></div>
<div style="line-height: 22.4px;"><span
style="line-height: 22.4px;"><br>
</span></div>
<div style="line-height: 22.4px;"><span
style="font-family: Verdana, 微软雅黑, 宋体, sans-serif;
line-height: 22.4px;">The attachment is our </span><span
style="line-height: 1.6;">projections.mhd</span><span
style="line-height: 1.6;"> <font face="Verdana, 微软雅黑,
宋体, sans-serif">file and we are running the latest
RTK, </font></span><span style="line-height: 1.6;">example
data works well.</span></div>
<div style="line-height: 22.4px;"><font face="Verdana,
微软雅黑, 宋体, sans-serif">I have another question about
our sphase.txt file. As my understanding of 4D
reconstruction process, </font><font face="Verdana,
微软雅黑, 宋体, sans-serif">spase.txt file should be
the optimal fit </font><span style="line-height: 1.6;">respiration
signals. But in our file, it only has 6 cycles, which
is impossible, </span>it confused me.</div>
<div style="line-height: 22.4px;">I'm now testing your new
code with our data, hope it works!</div>
<div style="line-height: 22.4px;">Thanks for your help.</div>
<div style="line-height: 22.4px;">
<blockquote type="cite"
cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr"
style="line-height: 22.4px;">
<blockquote type="cite"
cite="mid:88BEDC3F-802B-4D7D-A627-C28A26D68ED5@siat.ac.cn">
<div style="line-height: 1.6;">
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<p class="MsoNormal" style="margin: 0cm 0cm
0.0001pt; font-family: 'Times New Roman',
serif;"><span style="font-family: Verdana,
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</span></p>
<p class="MsoNormal" style="margin: 0cm 0cm
0.0001pt; font-family: 'Times New Roman',
serif;"><span style="font-family: Verdana,
sans-serif;">Regards</span></p>
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<p class="MsoNormal" style="margin: 0cm 0cm
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sans-serif;">Ruoyan Meng</span></p>
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<div
style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On
<span class="mail-date">1/9/2018 20:48</span>，<a
class="mail-to"
style="text-decoration:none;color:#2a83f2;"
href="mailto:cyril.mory@creatis.insa-lyon.fr"
moz-do-not-send="true">Cyril
Mory<cyril.mory@creatis.insa-lyon.fr></a> wrote： </div>
</div>
<blockquote id="ntes-pcmail-quote" style="margin: 0; padding:
0; font-size: 14px; font-family: '微软雅黑';">
<p>Hi again Ruoyan,</p>
<p><br>
</p>
<p>I have investigated further and found the source of the
problem: the code performs a rounding of the phase signal
to two digits, which for some values of your phase ended
up to be 1. And the rest of the code assumes that the
phase belongs to [0; 1[, i.e. there should never be a
value 1. <br>
The rounding is useful for optimization: projections with
identical phases can be forward and backprojected
together, which is faster than one-by-one, and with
high-precision phase values, there are never two equal
phase values. </p>
<p><br>
</p>
<p>So I just fixed the bug by setting the phase to 0 when
its rounding is equal to 1, which should do the trick. The
pull request is being tested, it should be merged soon. <br>
</p>
<p><br>
</p>
<p>Thanks for reporting your issue.<br>
</p>
<p>Regards,</p>
<p>Cyril<br>
</p>
<br>
<div class="moz-cite-prefix">On 09/01/2018 11:31, Cyril Mory
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<p>Hi Ruoyan,</p>
<p><br>
</p>
<p>I've had a look at your file sphase.txt, it looks
perfectly fine to me. The problem must lie elsewhere.
Does the application 4D ROOSTER work with the example
data provided on the wiki ? If it does, then the problem
lies in your data. In that case, please run</p>
<p><br>
</p>
<p>rtkprojections --path D:\bd\20171116 --regexp .*.his -o<span
style="line-height: 1.6;">D:\bd\20171116\</span><span
style="line-height: 1.6;">projections.mhd </span></p>
</blockquote>
<blockquote type="cite"
cite="mid:66e33d08-af6f-0d34-d5c4-628ad91a157c@creatis.insa-lyon.fr">
<p><br>
</p>
<p>and send us the "projections.mhd" file. It will contain
only the metadata of your projections, and we'll be able
to run the same command line as you and try to reproduce
the problem.</p>
<p><br>
</p>
<p>If, on the other hand, it doesn't even work with the
example data provided on the wiki, it is a software
problem. In that case, can you first update to the
latest RTK (the git master branch), recompile and test
again ?</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Cyril<br>
</p>
<br>
<div class="moz-cite-prefix">On 26/12/2017 10:47, ry.meng
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:88BEDC3F-802B-4D7D-A627-C28A26D68ED5@siat.ac.cn">
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<div><span>Hi</span></div>
<div><span><br>
</span></div>
<div><span>Thank you for your reply. I have checked
the value in sphase.txt and don't have any
value </span><span style="font-family: Verdana,
微软雅黑, 宋体, sans-serif; line-height: 22.4px;">larger
or equal to 5. </span><font face="Verdana, 微软雅黑,
宋体, sans-serif">Maybe the problem lies
elsewhere? Thanks.</font></div>
<div><br>
</div>
<div>
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Verdana, 微软雅黑, 宋体, sans-serif;">
<p class="MsoNormal" style="margin: 0cm 0cm
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<div style="line-height: 22.4px; font-family:
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<p class="MsoNormal" style="margin: 0cm 0cm
0.0001pt; font-family: 'Times New Roman',
serif;"><span style="font-family: Verdana,
sans-serif;">Ruoyan Meng</span></p>
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<div
style="font-size:14px;line-height:1.5;word-break:break-all;margin-left:10px;margin-right:10px">On
<span class="mail-date">12/26/2017 17:14</span>，<a
class="mail-to"
style="text-decoration:none;color:#2a83f2;"
href="mailto:simon.rit@creatis.insa-lyon.fr"
moz-do-not-send="true">Simon
Rit<simon.rit@creatis.insa-lyon.fr></a>
wrote： </div>
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<blockquote id="ntes-pcmail-quote" style="margin: 0;
padding: 0; font-size: 14px; font-family: '微软雅黑';">
<div dir="ltr">
<div>
<div>Hi,<br>
</div>
If you look at the <a
href="https://github.com/SimonRit/RTK/blob/master/code/rtkPhasesToInterpolationWeights.hxx#L154"
moz-do-not-send="true">code</a>, you'll see
that the error message corresponds to the case
where you have a phase which equals the number
of frames. This cannot be since it is 0-based.
In other words, with the option "--frames 5",
you cannot have a value larger or equal to 5 in
your file sphase.txt.<br>
</div>
Simon<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Dec 25, 2017 at
9:36 AM, ry.meng <span dir="ltr"><<a
href="mailto:ry.meng@siat.ac.cn"
target="_blank" moz-do-not-send="true">ry.meng@siat.ac.cn</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div>
<div
style="font-family:"\005fae\008f6f\0096c5\009ed1";line-height:1.6">
<div><span><br>
</span></div>
<div><span>Hi:</span></div>
<div><span> </span></div>
<div>When I tried the application of 4D
ROOSTER Reconstruction with my own data,
it will stop for the following reason: <span
style="line-height:22.4px">problem
while determining the interpolation
weights</span><span
style="line-height:1.6">. Maybe you
guys have met this problem before and
have a solution for it. Thank you very
much and I hope to receive your reply
soon.</span></div>
<div>
<div
style="font-family:Verdana,微软雅黑,宋体,sans-serif;line-height:22.4px">
<p class="MsoNormal"
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Roman',serif;margin:0cm 0cm
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</span></font></p>
<p class="MsoNormal"
style="font-family:'Times New
Roman',serif;margin:0cm 0cm
0.0001pt"><font
style="font-size:14px" size="2"><span
style="font-family:Verdana,sans-serif">Happy Holidays!</span></font></p>
<p class="MsoNormal"
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0.0001pt"><font
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</span></font></p>
<p class="MsoNormal"
style="font-family:'Times New
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0.0001pt"><font
style="font-size:14px" size="2"><span
style="font-family:Verdana,sans-serif">Regards</span></font></p>
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<p class="MsoNormal"
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0.0001pt"><font
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style="font-family:Verdana,sans-serif">Ruoyan Meng</span></font></p>
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<p class="MsoNormal"
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<div
style="font-family:Verdana,微软雅黑,宋体,sans-serif;line-height:22.4px">
<p class="MsoNormal"
style="font-family:'Times New
Roman',serif;margin:0cm 0cm
0.0001pt"><font
style="font-size:12px" size="2"><span
style="font-family:Verdana,sans-serif">------------------------------<wbr>------------------------------<wbr>------------------------------</span></font></p>
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style="font-family:'Times New
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0.0001pt"><span
style="font-family:Verdana,sans-serif"><font
style="font-size:12px" size="2">Research
Center for Medical Robotics and
Minimally Invasive Surgical
Devices,<br
style="font-family:Verdana,微软雅黑,宋体,sans-serif!important">
Institute of Biomedical and
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